Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1658 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg0803656534 sf0803655537 8 3656534 1.96E-10 2.62E-08
vg0134272325 sf0134271282 1 34272325 1.42E-09 1.42E-07
vg0402180766 sf0402176361 4 2180766 8.84E-08 NA
vg1217198477 sf1217192432 12 17198477 1.59E-06 NA
vg0415147095 sf0415137809 4 15147095 NA 3.46E-06
vg0415147115 sf0415137829 4 15147115 NA 8.41E-06